Python readCSV 예제들

예제 #1

 def test_writeCSV(self):
     read_csv_data = bioio.readCSV(['sample1.csv'])['sample1']
     bioio.writeCSV('rewritten_sample1.csv', read_csv_data)
     self.assertEqual(
         bioio.readCSV(['rewritten_sample1.csv'])['rewritten_sample1'],
         read_csv_data)
     os.remove('rewritten_sample1.csv')

예제 #2

 def test_readCSV(self):
     self.assertDictEqual(bioio.readCSV(example_csv_files),
                          expected_csv_input)
     with self.assertRaises(SystemExit):
         bioio.readCSV(['sample1.csv', 'path/sample2.csv'])
     with self.assertRaises(SystemExit):
         bioio.readCSV(['sample1.csv', 'sample2.txt'])

예제 #3

# -*- coding: utf-8 -*-
"""
@author: rishijavia
"""

import sys
import os

sys.path.append(os.path.join(sys.path[0], 'lib'))
sys.path.append(os.path.join(sys.path[0], 'test'))
import bioio
import biomath

# strip file extension and read file
read_csv = bioio.readCSV([sys.argv[-1]])
input_csv_name = sys.argv[-1][:-4]
input_csv_data = read_csv[input_csv_name]

# break the clusters
output_data = bioio.breakClusters(input_csv_data)

# write the resulting data to files
output_txt_name = input_csv_name + "_brokenCluster.txt"
bioio.writeTXT(output_txt_name, output_data)

예제 #4

파일: findLongestSeq.py 프로젝트: WatzekDigitalInitiatives/informatix

# -*- coding: utf-8 -*-
"""
@author: thatbudakguy
"""

import sys
import os
sys.path.append(os.path.join(sys.path[0],'lib'))
sys.path.append(os.path.join(sys.path[0],'test'))
import bioio
import biomath

# strip file extension and read file
read_csv = bioio.readCSV([sys.argv[-1]])
input_csv_name = sys.argv[-1][:-4]
input_csv_data = read_csv[input_csv_name]

# find longest sequences and get their corresponding ids
output_csv_data = biomath.findLongestSeq(input_csv_data)
output_seq_ids = bioio.splitCSV(output_csv_data)['output_seq_ids']
output_seqs = bioio.splitCSV(output_csv_data)['output_seqs']
output_seq_ids_txt = bioio.addGreaterThans(output_seq_ids)

# define names of the resulting files
output_csv_name = input_csv_name+"_trimmed.csv"
output_txt_name = input_csv_name+"_names_only.txt"
output_fasta_name = input_csv_name+".fasta"

# write the resulting data to files
bioio.writeCSV(output_csv_name,output_csv_data)
bioio.writeTXT(output_txt_name,output_seq_ids_txt)

예제 #5

 def test_splitCSV(self):
     example_input_csv = bioio.readCSV(['sample1.csv'])
     example_input_csv = bioio.splitCSV(example_input_csv['sample1'])
     self.assertDictEqual(example_input_csv, expected_split_data)

예제 #6

파일: unittests.py 프로젝트: WatzekDigitalInitiatives/informatix

 def test_writeCSV(self):
     read_csv_data = bioio.readCSV(['sample1.csv'])['sample1']
     bioio.writeCSV('rewritten_sample1.csv',read_csv_data)
     self.assertEqual(bioio.readCSV(['rewritten_sample1.csv'])['rewritten_sample1'],read_csv_data)
     os.remove('rewritten_sample1.csv')

예제 #7

파일: unittests.py 프로젝트: WatzekDigitalInitiatives/informatix

 def test_splitCSV(self):
     example_input_csv = bioio.readCSV(['sample1.csv'])
     example_input_csv = bioio.splitCSV(example_input_csv['sample1'])
     self.assertDictEqual(example_input_csv,expected_split_data)

예제 #8

파일: unittests.py 프로젝트: WatzekDigitalInitiatives/informatix

 def test_readCSV(self):
     self.assertDictEqual(bioio.readCSV(example_csv_files),expected_csv_input)
     with self.assertRaises(SystemExit):
         bioio.readCSV(['sample1.csv','path/sample2.csv'])
     with self.assertRaises(SystemExit):
         bioio.readCSV(['sample1.csv','sample2.txt'])